Pardon the spam, I forgot to include the list. Best, David 2012/9/5 David Westergaard <david at="" harsk.dk="">: > Hi Sean, > > Groups 1, 2 and 3 are no different except for the diet being fed. > > Best, > David > > 2012/9/5 Sean Davis <sdavis2 at="" mail.nih.gov="">: >> >> >> On Wed, Sep 5, 2012 at 4:55 AM, David Westergaard <david at="" harsk.dk=""> wrote: >>> >>> Hello, >>> >>> I am assisting in the setup of an experiment, in which 3 groups, each >>> consisting of 8 subjects, will be fed 3 diets: >>> Group 1 - Diet A >>> Group 2 - Diet B >>> Group 3 - Diet C >>> >>> We plan on using limma to identify the differentially expressed genes. >>> Reading the limma users guide, a factorial design matrix seems to be >>> appropriate. I am, however, wondering if we, by using this setup, can >>> elucidate the differentially expressed genes for each diet, and not >>> just the ones between groups, e.g. when comparing Group 1 - Group 2. >>> >>> What is your advice on this? >> >> >> Hi, David. >> >> Are groups 1, 2, and 3 different, or do they differ only in the diet being >> fed? >> >> Sean

On Wed, Sep 5, 2012 at 5:41 AM, David Westergaard <david@harsk.dk> wrote: > Pardon the spam, I forgot to include the list. > > Best, > David > > 2012/9/5 David Westergaard <david@harsk.dk>: > > Hi Sean, > > > > Groups 1, 2 and 3 are no different except for the diet being fed. > Then, I do not think this is a factorial design (in the sense of having two or more factors potentially interacting). You have only one factor, diet. The factor happens to have three levels, but it is still only one factor. Hope that helps, Sean > > > > Best, > > David > > > > 2012/9/5 Sean Davis <sdavis2@mail.nih.gov>: > >> > >> > >> On Wed, Sep 5, 2012 at 4:55 AM, David Westergaard <david@harsk.dk> > wrote: > >>> > >>> Hello, > >>> > >>> I am assisting in the setup of an experiment, in which 3 groups, each > >>> consisting of 8 subjects, will be fed 3 diets: > >>> Group 1 - Diet A > >>> Group 2 - Diet B > >>> Group 3 - Diet C > >>> > >>> We plan on using limma to identify the differentially expressed genes. > >>> Reading the limma users guide, a factorial design matrix seems to be > >>> appropriate. I am, however, wondering if we, by using this setup, can > >>> elucidate the differentially expressed genes for each diet, and not > >>> just the ones between groups, e.g. when comparing Group 1 - Group 2. > >>> > >>> What is your advice on this? > >> > >> > >> Hi, David. > >> > >> Are groups 1, 2, and 3 different, or do they differ only in the diet > being > >> fed? > >> > >> Sean > > _______________________________________________ > Bioconductor mailing list > Bioconductor@r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]